# Loughney et al., "Tectonic influence on Cenozoic mammal richness and sedimentation history of the Basin and Range, western North America"
# Science Advances
# Changepoint code and output

# load required package
library(changepoint)

# load files
macrostrat <- read.csv("macrostrat_June-2021.csv", header = TRUE, stringsAsFactors = FALSE)
macrostrat_nonfossil <- read.csv("macrostrat_nonfossil_June-2021", header = TRUE, stringsAsFactors = FALSE)
fossils <- read.csv("fossiliferous_units_January-2021.csv", header = TRUE, stringsAsFactors = FALSE)
deformation <- read.csv("deformation_rates_January-2021.csv", header = TRUE, stringsAsFactors = FALSE)
area <- read.csv("area_change.csv", header = TRUE, stringsAsFactors = FALSE)

# calculate sediment-accumulation rate (SAR) of fossiliferous Macrostrat packages
macrostrat_fossil_BRsar <- macrostrat$BR_SAR - macrostrat_nonfossil$BR_SAR
macrostrat_fossil_NBsar <- macrostrat$NB_SAR - macrostrat_nonfossil$NB_SAR
macrostrat_fossil_CBsar <- macrostrat$CB_SAR - macrostrat_nonfossil$CB_SAR
macrostrat_fossil_SBsar <- macrostrat$SB_SAR - macrostrat_nonfossil$SB_SAR

# calculate SAR of fossiliferous units of the Basin and Range
brfossilsar <- fossils$NB_SAR + fossils$CB_SAR + fossils$SB_SAR

# calculate changepoints
# -------------------------------------------------------------------------------------------------------------------------------
# BR 
# deformation rates
> brdef_mean_cusum_none <- cpt.mean(deformation$BR_rate, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> brdef_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 46 #22.5 - 23 Ma

> param.est(brdef_mean_cusum_none)
$mean
[1] 90.86515 21.94812

> t.test(deformation$BR_rate[1:46], deformation$BR_rate[47:72])

	Welch Two Sample t-test

data:  deformation$BR_rate[1:46] and deformation$BR_rate[47:72]
t = 9.4951, df = 63.505, p-value = 8.408e-14
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 54.41505 83.41902
sample estimates:
mean of x mean of y 
 90.86515  21.94812 

# area-change rates
> brarea_mean_cusum_none <- cpt.mean(area$BR_rate_change_sum, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> brarea_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 37 #18 - 18.5 Ma

> param.est(brarea_mean_cusum_none)
$mean
[1] 1784.351  631.982

> t.test(area$BR_rate_change_sum[1:37], area$BR_rate_change_sum[38:72])

	Welch Two Sample t-test

data:  area$BR_rate_change_sum[1:37] and area$BR_rate_change_sum[38:72]
t = 16.489, df = 48.447, p-value < 2.2e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 1011.884 1292.853
sample estimates:
mean of x mean of y 
 1784.351   631.982 

# SAR of all Macrostrat packages to 0 Ma
> brmacro_mean_cusum_none <- cpt.mean(macrostrat$BR_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> brmacro_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 8 # 3.5 - 4 Ma

> param.est(brmacro_mean_cusum_none)
$mean
[1] 29722.549  2847.446

> t.test(macrostrat$BR_SAR[1:8], macrostrat$BR_SAR[9:72])

	Welch Two Sample t-test

data:  macrostrat$BR_SAR[1:8] and macrostrat$BR_SAR[9:72]
t = 1.1634, df = 7.001, p-value = 0.2828
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -27747.08  81497.29
sample estimates:
mean of x mean of y 
29722.549  2847.446 

# SAR of all Macrostrat packages to 0.5 Ma
> brmacro_mod_mean_cusum_none <- cpt.mean(macrostrat$BR_SAR[2:72], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> brmacro_mod_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 35 # 17.5 - 18 Ma

> param.est(brmacro_mod_mean_cusum_none)
$mean
[1] 4806.873 1679.433

> t.test(macrostrat$BR_SAR[2:36], macrostrat$BR_SAR[37:72])

	Welch Two Sample t-test

data:  macrostrat$BR_SAR[2:36] and macrostrat$BR_SAR[37:72]
t = 10.776, df = 46.389, p-value = 3.213e-14
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 2543.394 3711.485
sample estimates:
mean of x mean of y 
 4806.873  1679.433 

# SAR of nonfossiliferous Macrostrat packages to 0 Ma
> brmacrononfoss_mean_cusum_none <- cpt.mean(macrostrat_nonfossil$BR_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> brmacrononfoss_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 8 # 3.5 - 4 Ma

> param.est(brmacrononfoss_mean_cusum_none)
$mean
[1] 28496.210  1460.846

> t.test(macrostrat_nonfossil$BR_SAR[1:8], macrostrat_nonfossil$BR_SAR[9:72])

	Welch Two Sample t-test

data:  macrostrat_nonfossil$BR_SAR[1:8] and macrostrat_nonfossil$BR_SAR[9:72]
t = 1.163, df = 7.0002, p-value = 0.2829
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -27933.17  82003.89
sample estimates:
mean of x mean of y 
28496.210  1460.846 

# SAR of nonfossiliferous Macrostrat packages to 0.5 Ma
> brmacrononfoss_mod_mean_cusum_none <- cpt.mean(macrostrat_nonfossil$BR_SAR[2:72], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> brmacrononfoss_mod_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 14 # 7 - 7.5 Ma

> param.est(brmacrononfoss_mod_mean_cusum_none)
$mean
[1] 3770.182 1360.421

> t.test(macrostrat_nonfossil$BR_SAR[2:15], macrostrat_nonfossil$BR_SAR[16:72])

	Welch Two Sample t-test

data:  macrostrat_nonfossil$BR_SAR[2:15] and macrostrat_nonfossil$BR_SAR[16:72]
t = 4.0245, df = 13.673, p-value = 0.001312
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 1122.623 3696.900
sample estimates:
mean of x mean of y 
 3770.182  1360.421 

# SAR of fossiliferous Macrostrat packages to 0 Ma
> brmacrofosssar_mean_cusum_none <- cpt.mean(macro_fossil_BRsar, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> brmacrofosssar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 34 # 16.5 - 17 Ma

> param.est(brmacrofosssar_mean_cusum_none)
$mean
[1] 2266.5069  565.5751

> t.test(macro_fossil_BRsar[1:34], macro_fossil_BRsar[35:72])

	Welch Two Sample t-test

data:  macro_fossil_BRsar[1:34] and macro_fossil_BRsar[35:72]
t = 11.76, df = 48.84, p-value = 7.449e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 1410.243 1991.621
sample estimates:
mean of x mean of y 
2266.5069  565.5751 

# SAR of fossiliferous units to 0 Ma
> brfossilsar_mean_cusum_none <- cpt.mean(brfossilsar, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> brfossilsar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 34 # 16.5 - 17 Ma

> param.est(brfossilsar_mean_cusum_none)
$mean
[1] 2942.3809  666.4261

> t.test(brfossilsar[1:34], brfossilsar[35:72])

	Welch Two Sample t-test

data:  brfossilsar[1:34] and brfossilsar[35:72]
t = 14.378, df = 46.647, p-value < 2.2e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 1957.445 2594.465
sample estimates:
mean of x mean of y 
2942.3809  666.4261 

# total number of mammal species 0 Ma
> brspall_mean_cusum_none <- cpt.mean(brAllRichness[ , 2], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> brspall_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 35 # 17 - 17.5 Ma

> param.est(brspall_mean_cusum_none)
$mean
[1] 43.428571  2.486486

> t.test(brAllRichness[1:35, 2], brAllRichness[36:72, 2])

	Welch Two Sample t-test

data:  brAllRichness[1:35, 2] and brAllRichness[36:72, 2]
t = 7.4435, df = 35.243, p-value = 9.891e-09
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 29.77843 52.10574
sample estimates:
mean of x mean of y 
43.428571  2.486486 

# ----------------------------------------------------------------------------------------------------------------------------------
# NB
# deformation rates
> nbdef_mean_cusum_none <- cpt.mean(deformation$NB_rate, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> nbdef_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 33 #16 - 16.5 Ma

> param.est(nbdef_mean_cusum_none)
$mean
[1] 25.75348 12.84556

> t.test(deformation$NB_rate[1:33], deformation$NB_rate[34:72])

	Welch Two Sample t-test

data:  deformation$NB_rate[1:33] and deformation$NB_rate[34:72]
t = 9.1678, df = 58.037, p-value = 6.978e-13
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 10.08961 15.72623
sample estimates:
mean of x mean of y 
 25.75348  12.84556 

# area-change rates
> nbarea_mean_cusum_none <- cpt.mean(area$NB_rate_change_sum, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> nbarea_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 35 #17 - 17.5 Ma

> param.est(nbarea_mean_cusum_none)
$mean
[1] 941.0916 540.4215

> t.test(area$NB_rate_change_sum[1:35], area$NB_rate_change_sum[36:72])

	Welch Two Sample t-test

data:  area$NB_rate_change_sum[1:35] and area$NB_rate_change_sum[36:72]
t = 10.227, df = 66.334, p-value = 2.871e-15
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 322.4570 478.8832
sample estimates:
mean of x mean of y 
 941.0916  540.4215 

# SAR of all Macrostrat packages to 0 Ma
> nbmacrosar_mean_cusum_none <- cpt.mean(macrostrat$NB_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> nbmacrosar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 33 # 16 - 16.5 Ma

> param.est(nbmacrosar_mean_cusum_none)
$mean
[1] 2673.3853  394.5177

> t.test(macrostrat$NB_SAR[1:33], macrostrat$NB_SAR[34:72])
	
	Welch Two Sample t-test

data:  macrostrat$NB_SAR[1:33] and macrostrat$NB_SAR[34:72]
t = 2.8509, df = 32.524, p-value = 0.007513
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
  651.6486 3906.0866
sample estimates:
mean of x mean of y 
2673.3853  394.5177 

# SAR of all Macrostrat packages to 0.5 Ma
> nbmacrosar_mod_mean_cusum_none <- cpt.mean(macrostrat$NB_SAR[2:72], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> nbmacrosar_mod_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 35 # 17.5 - 18 Ma

> param.est(nbmacrosar_mod_mean_cusum_none)
$mean
[1] 1806.444  342.440

> t.test(macrostrat$NB_SAR[2:36], macrostrat$NB_SAR[37:72])

	Welch Two Sample t-test

data:  macrostrat$NB_SAR[2:36] and macrostrat$NB_SAR[37:72]
t = 13.962, df = 66.656, p-value < 2.2e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 1254.698 1673.311
sample estimates:
mean of x mean of y 
 1806.444   342.440 

# SAR of nonfossiliferous Macrostrat packages to 0 Ma
> nbmacrononfossil_mean_cusum_none <- cpt.mean(macrostrat_nonfossil$NB_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> nbmacrononfossil_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 3 # 1 - 1.5 Ma

> param.est(nbmacrononfossil_mean_cusum_none)
$mean
[1] 9906.8793  577.1981

> t.test(macrostrat_nonfossil$NB_SAR[1:3], macrostrat_nonfossil$NB_SAR[4:72])

	Welch Two Sample t-test

data:  macrostrat_nonfossil$NB_SAR[1:3] and macrostrat_nonfossil$NB_SAR[4:72]
t = 1.0327, df = 2.0001, p-value = 0.4103
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -29539.95  48199.31
sample estimates:
mean of x mean of y 
9906.8793  577.1981 

# SAR of nonfossiliferous Macrostrat packages to 0.5 Ma
> nbmacrononfossil_mod_mean_cusum_none <- cpt.mean(macrostrat_nonfossil$NB_SAR[2:72], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> nbmacrononfossil_mod_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 35 # 17.5 - 18 Ma

> param.est(nbmacrononfossil_mod_mean_cusum_none)
$mean
[1] 835.3323 342.6900

> t.test(macrostrat_nonfossil$NB_SAR[2:36], macrostrat_nonfossil$NB_SAR[37:72])

	Welch Two Sample t-test

data:  macrostrat_nonfossil$NB_SAR[2:36] and macrostrat_nonfossil$NB_SAR[37:72]
t = 6.0639, df = 60.983, p-value = 9.134e-08
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 330.1876 655.0970
sample estimates:
mean of x mean of y 
 835.3323  342.6900 

# SAR of fossiliferous Macrostrat packages to 0 Ma
> macrostrat_fossil_NBsar[54] <- 0
> nbmacrofossilsar_mean_cusum_none <- cpt.mean(macrostrat_fossil_NBsar, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> nbmacrofossilsar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 34 # 16.5 - 17 Ma

> param.est(nbmacrofossilsar_mean_cusum_none)
$mean
[1] 1002.047    0.000

> t.test(macrostrat_fossil_NBsar[1:34], macrostrat_fossil_NBsar[35:72])

	Welch Two Sample t-test

data:  macro_fossil_NBsar[1:34] and macro_fossil_NBsar[35:72]
t = 14.584, df = 33, p-value = 6.06e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
  862.2622 1141.8317
sample estimates:
mean of x mean of y 
 1002.047     0.000 

# SAR of fossiliferous units to 0 Ma
> nbfosssar_mean_cusum_none <- cpt.mean(fossils$NB_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> nbfosssar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 33 #16 - 16.5 Ma

> param.est(nbfosssar_mean_cusum_none)
$mean
[1] 1706.80000   26.07179

> t.test(fossils$NB_SAR[1:33], fossils$NB_SAR[34:72])

	Welch Two Sample t-test

data:  fossils$NB_SAR[1:33] and fossils$NB_SAR[34:72]
t = 17.148, df = 32.285, p-value < 2.2e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 1500.462 1904.827
sample estimates:
 mean of x  mean of y 
1728.71636   26.07179 

# total number of mammal species to 0 Ma
> nbspall_mean_cusum_none <- cpt.mean(nbAllRichness[ , 2], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> nbspall_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 35 # 17 - 17.5 Ma

> param.est(nbspall_mean_cusum_none)
$mean
[1] 13.74286  0.00000

> t.test(nbAllRichness[1:35, 2], nbAllRichness[36:72, 2])

	Welch Two Sample t-test

data:  nbAllRichness[1:35, 2] and nbAllRichness[36:72, 2]
t = 3.7221, df = 34, p-value = 0.0007125
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
  6.239358 21.246357
sample estimates:
mean of x mean of y 
 13.74286   0.00000 

# ------------------------------------------------------------------------------------------------------------------------------ 
# CB
# deformation rates
> cbdef_mean_cusum_none <- cpt.mean(deformation$CB_rate, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> cbdef_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 44 #21.5 - 22 Ma

> param.est(cbdef_mean_cusum_none)
$mean
[1] 55.482909  2.295321

> t.test(deformation$CB_rate[1:44], deformation$CB_rate[45:72])

	Welch Two Sample t-test

data:  deformation$CB_rate[1:44] and deformation$CB_rate[45:72]
t = 9.5092, df = 46.644, p-value = 1.71e-12
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 41.93306 64.44211
sample estimates:
mean of x mean of y 
55.482909  2.295321 

# area-change rates
> cbarea_mean_cusum_none <- cpt.mean(area$CB_rate_change_sum, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> cbarea_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 42 #20.5 - 21 Ma

> param.est(cbarea_mean_cusum_none)
$mean
[1] 805.1337 204.9367

> t.test(area$CB_rate_change_sum[1:42], area$CB_rate_change_sum[43:72])

	Welch Two Sample t-test

data:  area$CB_rate_change_sum[1:42] and area$CB_rate_change_sum[43:72]
t = 19.906, df = 69.309, p-value < 2.2e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 540.0502 660.3436
sample estimates:
mean of x mean of y 
 805.1337  204.9367 

# SAR of all Macrostrat packages to 0 Ma
> cbmacrosar_mean_cusum_none <- cpt.mean(macrostrat$CB_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> cbmacrosar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 15 # 7 - 7.5 Ma 

> param.est(cbmacrosar_mean_cusum_none)
$mean
[1] 4733.103  719.077

> t.test(macrostrat$CB_SAR[1:15], macrostrat$CB_SAR[16:72])

	Welch Two Sample t-test

data:  macrostrat$CB_SAR[1:15] and macrostrat$CB_SAR[16:72]
t = 2.034, df = 14.04, p-value = 0.0613
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -217.5471 8245.5986
sample estimates:
mean of x mean of y 
 4733.103   719.077 

# SAR of all Macrostrat packages to 0.5 Ma
> cbmacrosar_mod_mean_cusum_none <- cpt.mean(macrostrat$CB_SAR[2:72], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> cbmacrosar_mod_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 18 # 9 - 9.5 Ma

> param.est(cbmacrosar_mod_mean_cusum_none)
$mean
[1] 2461.7285  682.5349

> t.test(macrostrat$CB_SAR[2:19], macrostrat$CB_SAR[20:72])

	Welch Two Sample t-test

data:  macrostrat$CB_SAR[2:19] and macrostrat$CB_SAR[20:72]
t = 4.0224, df = 18.036, p-value = 0.0007962
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
  850.0424 2708.3448
sample estimates:
mean of x mean of y 
2461.7285  682.5349 

# SAR of nonfossiliferous Macrostrat packages to 0 Ma
> cbmacro_nonfossilsar_mean_cusum_none <- cpt.mean(macrostrat_nonfossil$CB_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> cbmacro_nonfossilsar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 10 # 4.5 - 5 Ma

> param.est(cbmacro_nonfossilsar_mean_cusum_none)
$mean
[1] 5844.1515  310.2435

> t.test(macrostrat_nonfossil$CB_SAR[1:10], macrostrat_nonfossil$CB_SAR[11:72])

	Welch Two Sample t-test

data:  macrostrat_nonfossil$CB_SAR[1:10] and macrostrat_nonfossil$CB_SAR[11:72]
t = 1.8857, df = 9.0052, p-value = 0.09195
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -1104.328 12172.144
sample estimates:
mean of x mean of y 
5844.1515  310.2435 

# SAR of nonfossiliferous Macrostrat packages to 0.5 Ma
> cbmacro_nonfossilsar_mod_mean_cusum_none <- cpt.mean(macrostrat_nonfossil$CB_SAR[2:72], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> cbmacro_nonfossilsar_mod_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 14 # 7 - 7.5 Ma

> param.est(cbmacro_nonfossilsar_mod_mean_cusum_none)
$mean
[1] 2307.3380  243.4283

> t.test(macrostrat_nonfossil$CB_SAR[2:15], macrostrat_nonfossil$CB_SAR[16:72])

	Welch Two Sample t-test

data:  macrostrat_nonfossil$CB_SAR[2:15] and macrostrat_nonfossil$CB_SAR[16:72]
t = 3.7069, df = 13.148, p-value = 0.002588
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
  862.4461 3265.3733
sample estimates:
mean of x mean of y 
2307.3380  243.4283 

# SAR of fossiliferous Macrostrat packages to 0 Ma
> cbmacro_fossilsar_mean_cusum_none <- cpt.mean(macrostrat_fossil_CBsar, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> cbmacro_fossilsar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 49 # 24 - 24.5 Ma

> param.est(cbmacro_fossilsar_mean_cusum_none)
$mean
[1] 627.1222 155.5797

> t.test(macro_fossil_CBsar[1:49], macro_fossil_CBsar[50:72])

	Welch Two Sample t-test

data:  macro_fossil_CBsar[1:49] and macro_fossil_CBsar[50:72]
t = 9.3569, df = 56.855, p-value = 4.156e-13
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 370.6220 572.4629
sample estimates:
mean of x mean of y 
 627.1222  155.5797 

# SAR of fossiliferous units to 0 Ma
> cbfosssar_mean_cusum_none <- cpt.mean(fossils$CB_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> cbfosssar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 47 #23 - 23.5 Ma

> param.est(cbfosssar_mean_cusum_none)
$mean
[1] 550.6909 102.1260

> t.test(fossils$CB_SAR[1:47], fossils$CB_SAR[48:72])

	Welch Two Sample t-test

data:  fossils$CB_SAR[1:47] and fossils$CB_SAR[48:72]
t = 10.227, df = 51.349, p-value = 5.512e-14
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 360.5254 536.6043
sample estimates:
mean of x mean of y 
 550.6909  102.1260 
 
# total number of species to 0 Ma
> cbspall_mean_cusum_none <- cpt.mean(cbAllRichness[ , 2], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> cbspall_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 34 # 16.5 - 17 Ma

> param.est(cbspall_mean_cusum_none)
$mean
[1] 18.2647059  0.9210526

> t.test(cbAllRichness[1:34, 2], cbAllRichness[35:72, 2])

	Welch Two Sample t-test

data:  cbAllRichness[1:34, 2] and cbAllRichness[35:72, 2]
t = 5.8553, df = 33.949, p-value = 1.335e-06
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 11.32373 23.36358
sample estimates:
 mean of x  mean of y 
18.2647059  0.9210526 

# -----------------------------------------------------------------------------------------------------------------------------
# SB
# deformation rates
> sbdef_mean_cusum_none <- cpt.mean(deformation$SB_rate, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> sbdef_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 54 #26.5 - 27 Ma

> param.est(sbdef_mean_cusum_none)
$mean
[1] 15.998352  1.676556

> t.test(deformation$SB_rate[1:54], deformation$SB_rate[55:72])

	Welch Two Sample t-test

data:  deformation$SB_rate[1:54] and deformation$SB_rate[55:72]
t = 9.6622, df = 69.938, p-value = 1.649e-14
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 11.36550 17.27809
sample estimates:
mean of x mean of y 
15.998352  1.676556 

# area-change rates
> sbarea_mean_cusum_none <- cpt.mean(area$SB_rate_change_sum, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> sbarea_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 42 #20.5 - 21 Ma

> param.est(sbarea_mean_cusum_none)
$mean
[1] 1012.0226  424.9775

> t.test(area$SB_rate_change_sum[1:42], area$SB_rate_change_sum[43:72])

	Welch Two Sample t-test

data:  area$SB_rate_change_sum[1:42] and area$SB_rate_change_sum[43:72]
t = 8.324, df = 64.537, p-value = 8.165e-12
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 446.1792 727.9110
sample estimates:
mean of x mean of y 
1012.0226  424.9775 

# SAR of all Macrostrat packages to 0 Ma
> sbmacrosar_mean_cusum_none <- cpt.mean(macrostrat$SB_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> sbmacrosar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 2 # 0.5 - 1 Ma

> param.est(sbmacrosar_mean_cusum_none)
$mean
[1] 66501.517  1020.315

> t.test(macrostrat$SB_SAR[1:2], macrostrat$SB_SAR[3:72])

	Welch Two Sample t-test

data:  macrostrat$SB_SAR[1:2] and macrostrat$SB_SAR[3:72]
t = 1.0034, df = 1, p-value = 0.4989
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -763752.8  894715.2
sample estimates:
mean of x mean of y 
66501.517  1020.315 

# SAR of all Macrostrat packages to 0.5 Ma
> sbmacrosar_mod_mean_cusum_none <- cpt.mean(macrostrat$SB_SAR[2:72], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> sbmacrosar_mod_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 34 # 17 - 17.5 Ma

> param.est(sbmacrosar_mod_mean_cusum_none)
$mean
[1] 1225.214  837.946

> t.test(macrostrat$SB_SAR[2:35], macrostrat$SB_SAR[36:72])

	Welch Two Sample t-test

data:  macrostrat$SB_SAR[2:35] and macrostrat$SB_SAR[36:72]
t = 4.7885, df = 47.168, p-value = 1.702e-05
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 224.5843 549.9524
sample estimates:
mean of x mean of y 
 1225.214   837.946 

# SAR of nonfossiliferous Macrostrat packages to 0 Ma
> sbmacro_nonfossilsar_mean_cusum_none <- cpt.mean(macrostrat_nonfossil$SB_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> sbmacro_nonfossilsar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 2 # 0.5 - 1 Ma

> param.est(sbmacro_nonfossilsar_mean_cusum_none)
$mean
[1] 66243.2585   596.4771

> t.test(macrostrat_nonfossil$SB_SAR[1:2], macrostrat_nonfossil$SB_SAR[3:72])
	
	Welch Two Sample t-test

data:  macrostrat_nonfossil$SB_SAR[1:2] and macrostrat_nonfossil$SB_SAR[3:72]
t = 1.0034, df = 1, p-value = 0.4989
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -765613.6  896907.2
sample estimates:
 mean of x  mean of y 
66243.2585   596.4771 

# SAR of nonfossiliferous Macrostrat packages to 0.5 Ma
> sbmacro_nonfossilsar_mod_mean_cusum_none <- cpt.mean(macrostrat_nonfossil$SB_SAR[2:72], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> sbmacro_nonfossilsar_mod_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 52 # 26 - 26.5 Ma 

> param.est(sbmacro_nonfossilsar_mod_mean_cusum_none)
$mean
[1] 499.8758 872.7038

> t.test(macrostrat_nonfossil$SB_SAR[2:53], macrostrat_nonfossil$SB_SAR[54:72])

	Welch Two Sample t-test

data:  macrostrat_nonfossil$SB_SAR[2:53] and macrostrat_nonfossil$SB_SAR[54:72]
t = -2.799, df = 19.767, p-value = 0.01116
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -650.88663  -94.76934
sample estimates:
mean of x mean of y 
 499.8758  872.7038 

# SAR of fossiliferous Macrostrat packages to 0 Ma
> sbmacro_fossilsar_mean_cusum_none <- cpt.mean(macro_fossil_SBsar, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> sbmacro_fossilsar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 37 # 18 - 18.5 Ma

> param.est(sbmacro_fossilsar_mean_cusum_none)
$mean
[1] 622.4228 204.4437

> t.test(macro_fossil_SBsar[1:37], macro_fossil_SBsar[38:72])

	Welch Two Sample t-test

data:  macro_fossil_SBsar[1:37] and macro_fossil_SBsar[38:72]
t = 8.7674, df = 57.245, p-value = 3.583e-12
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 322.5216 513.4366
sample estimates:
mean of x mean of y 
 622.4228  204.4437 

# SAR of fossiliferous units to 0 Ma
> sbfosssar_mean_cusum_none <- cpt.mean(fossils$SB_SAR, method = "AMOC", test.stat = "CUSUM", penalty = "None")
> sbfosssar_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 49 #24 - 24.5 Ma

> param.est(sbfosssar_mean_cusum_none)
$mean
[1] 656.9629 290.1696

> t.test(fossils$SB_SAR[1:49], fossils$SB_SAR[50:72])

	Welch Two Sample t-test

data:  fossils$SB_SAR[1:49] and fossils$SB_SAR[50:72]
t = 5.3715, df = 38.612, p-value = 3.962e-06
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 228.6295 504.9570
sample estimates:
mean of x mean of y 
 656.9629  290.1696 
 
# total number of mammal species to 0 Ma
> sbspall_mean_cusum_none <- cpt.mean(sbAllRichness[ , 2], method = "AMOC", test.stat = "CUSUM", penalty = "None")
> sbspall_mean_cusum_none

Class 'cpt' : Changepoint Object
       ~~   : S4 class containing 12 slots with names
              cpttype date version data.set method test.stat pen.type pen.value minseglen cpts ncpts.max param.est 

Created on  : Sun Nov 01 20:55:53 2020 

summary(.)  :
----------
Created Using changepoint version 2.2.2 
Changepoint type      : Change in mean 
Method of analysis    : AMOC 
Test Statistic  : CUSUM 
Type of penalty       : None with value, 0 
Minimum Segment Length :  
Maximum no. of cpts   : 1 
Changepoint Locations : 33 # 16 - 16.5 Ma

> param.est(sbspall_mean_cusum_none)
$mean
[1] 22.727273  2.230769

> t.test(sbAllRichness[1:33, 2], sbAllRichness[34:72, 2])

	Welch Two Sample t-test

data:  sbAllRichness[1:33, 2] and sbAllRichness[34:72, 2]
t = 4.7216, df = 33.433, p-value = 4.07e-05
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 11.66895 29.32405
sample estimates:
mean of x mean of y 
22.727273  2.230769 
